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XChem group deposition -- Crystal Structure of human ACVR1 in complex with PK012456b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SRH 6SRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.394 α = 90 b = 84.763 β = 130.99 c = 88.19 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-01-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.3 66.65 73.7 0.061 1 17.8 126742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 4.7 0.78 0.39 400
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6SRH 1.3 66.57 120369 6373 73.72 0.1597 0.1587 0.1683 0.1802 0.1857 RANDOM 17.551
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.39 -0.25 -0.34 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 6.609 r_mcangle_it 2.704 r_angle_refined_deg 1.874 r_mcbond_it 1.776 r_mcbond_other 1.775 r_angle_other_deg 1.524 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 6.609 r_mcangle_it 2.704 r_angle_refined_deg 1.874 r_mcbond_it 1.776 r_mcbond_other 1.775 r_angle_other_deg 1.524 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4574 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing